Here is the fix for your problem..........SLOW DOWN.

If you choose not to slow down, then more than likely water is getting to the ignition system somewhere and making it miss. It could be plugs, wires, or distributor.....or possibly even getting into the wiring harness somewhere where there is a wire with some insulation missing and partially shorting it out (unlikely, but possible) They make a waterproofing spray you can spray on stuff (wires and cap) to keep water/moisture from affecting it.
It could also be water getting into the airbox area and if a little water is getting sucked into the engine, it will cause it to miss as well.